Introduction
- Literature and evidence review essential in public health practice
- Exponential growth in volume of literature
- Initial first steps usually:
- Developing search strategy
- Reviwing and filtering abstracts
- Obtaining full text (if possible)
- Data extraction
This can be a manual and protracted interative process which may involve using specialised searching services, downloading abstracts, reading and filtering, secondary searching and so on, and may involve sifting many thousands of abstracts.
Often we may just want a rapid overview of the literature to help focus further reviewing.
In this vignette we demonstrate the use of R packages for large scale extraction of abstracts, and analytical techniques for identifying topics or themes in the abstracts.
The vignette is based on a number of R packages:
europepmc- this is a sophisticated tool which interacts with the PubMedCentral API and provdes access to additional fields.adjutant- this is a fully fledged package with retrieval and clustering functions. 3.tidytext- a package for text mining using tidy data principles.
Rtsne- this uses the tSNE algorithm for data reduction and cluster visualisationdbscan- applies the HDBSCAN algorithm for data clusteringmyScrapers- wraps some functions built on other packages to automate the search, extraction, and filtering process.
We have “hacked” some of the functions in these packages and written additional functions to develop a work flow from searching and retrieval to analysis
A simple example using europepmc
Searching Europe PubMed Central (epmc)
This is a package which allows searching of EuropePMC via the API.
It can be downloaded from CRAN.
if(!require("europepmc")) install.packages("europepmc")
library(europepmc)The main function is epmc_search which allows us to search the site and retrieve abstracts, metadata and citation counts.
We’ll use it with the search term “big data” AND “public health”.
head(epmc_search(params$search, limit = 10))
#> # A tibble: 6 x 28
#> id source pmid doi title authorString journalTitle issue
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 3148~ MED 3148~ 10.1~ mHea~ Madanian S,~ BMJ Health ~ 1
#> 2 3109~ MED 3109~ 10.1~ Big ~ Zetino J, M~ Soc Work Pu~ <NA>
#> 3 3143~ MED 3143~ 10.3~ Usin~ Cassim N, M~ Stud Health~ <NA>
#> 4 3147~ MED 3147~ 10.1~ Usin~ Zhang Y, Ba~ Int J Biome~ <NA>
#> 5 3106~ MED 3106~ 10.1~ Auto~ Shaw D, Fav~ Med Health ~ <NA>
#> 6 3142~ MED 3142~ 10.1~ The ~ Kenney M, M~ Med Humanit <NA>
#> # ... with 20 more variables: journalVolume <chr>, pubYear <chr>,
#> # journalIssn <chr>, pubType <chr>, isOpenAccess <chr>, inEPMC <chr>,
#> # inPMC <chr>, hasPDF <chr>, hasBook <chr>, citedByCount <int>,
#> # hasReferences <chr>, hasTextMinedTerms <chr>,
#> # hasDbCrossReferences <chr>, hasLabsLinks <chr>,
#> # hasTMAccessionNumbers <chr>, firstIndexDate <chr>,
#> # firstPublicationDate <chr>, pageInfo <chr>, pmcid <chr>,
#> # hasSuppl <chr>This doesn’t extract the abstract text or Mesh headings (keywords) - to facilitate this we have wrapped the search function, into get_full_search in myScrapers.
library(tictoc)
tic()
search1 <- get_full_search(search = params$search, limit = params$limit)
toc()
#> 1751.07 sec elapsed
head(search1, 20)
#> # A tibble: 20 x 32
#> id source pmid doi title authorString journalTitle issue
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 3148~ MED 3148~ 10.1~ mHea~ Madanian S,~ BMJ Health ~ 1
#> 2 3109~ MED 3109~ 10.1~ Big ~ Zetino J, M~ Soc Work Pu~ <NA>
#> 3 3143~ MED 3143~ 10.3~ Usin~ Cassim N, M~ Stud Health~ <NA>
#> 4 3147~ MED 3147~ 10.1~ Usin~ Zhang Y, Ba~ Int J Biome~ <NA>
#> 5 3106~ MED 3106~ 10.1~ Auto~ Shaw D, Fav~ Med Health ~ <NA>
#> 6 3142~ MED 3142~ 10.1~ The ~ Kenney M, M~ Med Humanit <NA>
#> 7 3126~ MED 3126~ 10.2~ Topi~ Cho HW. Osong Publi~ 3
#> 8 3131~ MED 3131~ 10.1~ Big ~ Yang C, Kon~ Nephrology ~ <NA>
#> 9 3130~ MED 3130~ 10.1~ Use ~ Vermund SH. Lancet HIV 8
#> 10 3123~ MED 3123~ 10.3~ [Ran~ Xu L, Wang ~ Zhonghua Li~ 6
#> 11 3138~ MED 3138~ 10.1~ Data~ Hoeyer K, B~ Soc Stud Sci 4
#> 12 3109~ MED 3109~ 10.1~ Arti~ Leatherdale~ Cancer Caus~ 7
#> 13 3149~ MED 3149~ 10.1~ "Hea~ Cheng YC, H~ Drug Alcoho~ <NA>
#> 14 3133~ MED 3133~ 10.3~ Appl~ Kim H, Han ~ Int J Envir~ 14
#> 15 3110~ MED 3110~ 10.3~ Usin~ Rocklöv J, ~ Emerg Infec~ 6
#> 16 3141~ MED 3141~ 10.1~ Publ~ Rodríguez-G~ Yearb Med I~ 1
#> 17 3120~ MED 3120~ 10.1~ Does~ Caliebe A, ~ BMC Med Res~ 1
#> 18 3127~ MED 3127~ 10.1~ Data~ Hoeyer K. Soc Stud Sci 4
#> 19 3145~ MED 3145~ 10.1~ Why ~ Lehne M, Sa~ NPJ Digit M~ <NA>
#> 20 3127~ MED 3127~ 10.1~ Leve~ Thompson ME~ N C Med J 4
#> # ... with 24 more variables: journalVolume <chr>, pubYear <chr>,
#> # journalIssn <chr>, pubType <chr>, isOpenAccess <chr>, inEPMC <chr>,
#> # inPMC <chr>, hasPDF <chr>, hasBook <chr>, citedByCount <int>,
#> # hasReferences <chr>, hasTextMinedTerms <chr>,
#> # hasDbCrossReferences <chr>, hasLabsLinks <chr>,
#> # hasTMAccessionNumbers <chr>, firstIndexDate <chr>,
#> # firstPublicationDate <chr>, pageInfo <chr>, pmcid <chr>,
#> # hasSuppl <chr>, name <int>, absText <list>, mesh <list>,
#> # keywords <chr>We can see that the get_full_search function returns addition metadata such as citation counts, whether the journal is open access and whether there is PDF available. By default, 1000 article descriptions are downloaded. It also includes mesh headings and abstract text.
we can see how many articles are available altogether by running epmc_profile.
profile <- epmc_profile(query = params$search)
Running epmc_profile allows us to see that there are 4001 articles of which 3521 are full text articles, and 2457 are open access.
Analysing abstracts
Abstracts per year
We can easily look at annual abstract frequency - we can readily see the growth in publication frequency in the last 3 years.
search1 %>%
count(pubYear) %>%
ggplot(aes(pubYear, n)) +
geom_col(fill = "blue") +
labs(title = "Abstracts per year",
subtitle = paste("Search: ", params$search)) +
phecharts::theme_phe() +
theme(axis.text.x = element_text(angle = 45 ,hjust = 1))
Journal frequency
Similarly we can identify the most frequent journals
journal_count <- search1 %>%
count(journalTitle) %>%
top_n(20) %>%
arrange(-n)
journal_count %>%
ggplot(aes(reorder(journalTitle, n), n)) +
geom_col(fill = "blue") +
coord_flip() +
labs(title = "Journal frequency") +
phecharts::theme_phe()
PLoS One and Int J Environ Res Public Health are the most frequent journals publishing articles on “big data” AND “public health”.
Topic identification
Once we have a data frame of 4004 records with abstract text, we can prepare the data for analysis. THe create_corpus function is designed for this.
out1 <- search1 %>%
select(pmid, pmcid ,doi, title, pubYear, citedByCount, absText, journalTitle) %>%
filter(absText != "NULL") %>%
mutate(text = paste(title, absText))
Text mining
We will use a method exemplified in the adjutant package which uses unsupervised machine learning to try and cluster similar articles and attach themes.
In this approach undertake some natural language processing. We will
- Split each abstract into groups is single words
- Remove numbers and common (stop) words
- Stem each word (definition:)
- Calculate the tf-idf score for each word in each abstract - this gives more weight to words which are more “typical” of the abstracts
- Create a document feature matrix
- Undertake dimensionality reduction using tSNE to simplify
- Run HDBSCAN to identify clusters
- Name the clusters
- QA the result
The ultimate output of this analysis is a visualisation of clustered and labelled abstracts and a interactive table.
library(tidytext)
corp <- create_corpus(df = search1)
head(corp$corpus)
#> # A tibble: 6 x 6
#> pmid word n tf idf tf_idf
#> <chr> <chr> <int> <dbl> <dbl> <dbl>
#> 1 18769432 biocur 1 0.25 7.57 1.89
#> 2 18769432 data 1 0.25 0.466 0.117
#> 3 18769432 futur 1 0.25 1.83 0.457
#> 4 18769432 null 1 0.25 2.19 0.546
#> 5 21214922 accuraci 2 0.0185 3.03 0.0561
#> 6 21214922 aim 1 0.00926 1.88 0.0174
clust <- create_cluster(corpus = corp$corpus, minPts = 10)
#> 1640.52 sec elapsed
clust$cluster_size
#> # A tibble: 70 x 2
#> cluster n
#> <dbl> <int>
#> 1 0 1326
#> 2 1 62
#> 3 2 12
#> 4 3 49
#> 5 4 49
#> 6 5 13
#> 7 6 11
#> 8 7 37
#> 9 8 74
#> 10 9 42
#> # ... with 60 more rowsLabelling clusters
labels <- label_clusters(corp$corpus, clustering = clust$clustering, top_n = 4)
#> 1.08 sec elapsed
labels$labels
#> # A tibble: 70 x 2
#> # Groups: cluster [70]
#> cluster clus_names
#> <dbl> <chr>
#> 1 0 research-health-data-studi
#> 2 1 hiv-studi-data-health
#> 3 2 ehealth-care-health-inform-base-data
#> 4 3 pollut-air-studi-health
#> 5 4 vaccin-develop-data-health
#> 6 5 cancer-null-report-data
#> 7 6 pregnanc-popul-studi-data
#> 8 7 nutrit-approach-health-data
#> 9 8 imag-clinic-data-studi
#> 10 9 injuri-data-studi-health
#> # ... with 60 more rowsVisualise
p <- labels$results %>%
left_join(search1, by = c("pmid.value" = "pmid")) %>%
ggplot(aes(X1, X2)) +
geom_point(aes(colour = clustered, size = citedByCount) ) +
ggrepel::geom_text_repel(data = labels$plot, aes(medX, medY, label = clus_names), size = 3, colour = "#006d2c", alpha = 0.9)
p + scale_alpha_manual(values=c(1,0)) +
viridis::scale_color_viridis(discrete = TRUE, option = "cividis", alpha = .6) +
phecharts::theme_phe() +
theme(panel.background = element_rect(fill = "#f0f0f0")) +
labs(subtitle = paste("Clustering: ", nrow(labels$plot), " topics" ),
title = paste("Search ", "= ", params$search ))
Understanding the labels
Most cited articles
most_cited <- labels$results %>%
left_join(search1, by = c("pmid.value" = "pmid")) %>%
filter(cluster !=0) %>%
group_by(clus_names) %>%
top_n(n = 3, citedByCount) %>%
select(clus_names, title, pubYear, citedByCount) %>%
ungroup() %>%
arrange(clus_names, -citedByCount)
most_cited %>%
formattable::formattable()| clus_names | title | pubYear | citedByCount |
|---|---|---|---|
| abstract-meet-annual-null | Pandemic influenza and socioeconomic disparities: Lessons from 1918 Chicago. | 2016 | 4 |
| abstract-meet-annual-null | Oral abstracts of the 22nd International AIDS Conference, 23-27 July 2018, Amsterdam, the Netherlands. | 2018 | 4 |
| abstract-meet-annual-null | Abstracts from the 38th annual meeting of the society of general internal medicine. | 2015 | 3 |
| abstract-meet-annual-null | Proceedings of the 3rd Biennial Conference of the Society for Implementation Research Collaboration (SIRC) 2015: advancing efficient methodologies through community partnerships and team science : Seattle, WA, USA. 24-26 September 2015. | 2016 | 3 |
| ag-associ-risk-studi | Sex-age-specific association of body mass index with all-cause mortality among 12.8 million Korean adults: a prospective cohort study. | 2015 | 35 |
| ag-associ-risk-studi | Association Between Smoking and Physician-Diagnosed Stroke and Myocardial Infarction in Male Adults in Korea. | 2016 | 3 |
| ag-associ-risk-studi | Socioeconomic disparities in first stroke incidence, quality of care, and survival: a nationwide registry-based cohort study of 44 million adults in England. | 2018 | 3 |
| ag-nation-health-studi | Cohort profile: the National Health Insurance Service-National Health Screening Cohort (NHIS-HEALS) in Korea. | 2017 | 41 |
| ag-nation-health-studi | National dental policies and socio-demographic factors affecting changes in the incidence of periodontal treatments in Korean: A nationwide population-based retrospective cohort study from 2002-2013. | 2016 | 12 |
| ag-nation-health-studi | Longitudinal change in estimated GFR among CKD patients: A 10-year follow-up study of an integrated kidney disease care program in Taiwan. | 2017 | 8 |
| ag-popul-studi-result | Space-Time Covariation of Mortality with Temperature: A Systematic Study of Deaths in France, 1968-2009. | 2015 | 18 |
| ag-popul-studi-result | Multiscale Entropy of Electroencephalogram as a Potential Predictor for the Prognosis of Neonatal Seizures. | 2015 | 6 |
| ag-popul-studi-result | Maximising follow-up participation rates in a large scale 45 and Up Study in Australia. | 2016 | 5 |
| ai-artifici-intellig-health | Global Evolution of Research in Artificial Intelligence in Health and Medicine: A Bibliometric Study. | 2019 | 3 |
| ai-artifici-intellig-health | An overview of GeoAI applications in health and healthcare. | 2019 | 2 |
| ai-artifici-intellig-health | Digital Diabetes Data and Artificial Intelligence: A Time for Humility Not Hubris. | 2019 | 1 |
| ai-artifici-intellig-health | Artificial Intelligence for infectious disease Big Data Analytics. | 2019 | 1 |
| ai-artifici-intellig-health | Artificial Intelligence vs. Natural Stupidity: Evaluating AI readiness for the Vietnamese Medical Information System. | 2019 | 1 |
| analysi-approach-data-base | Meta-analysis in clinical trials revisited. | 2015 | 250 |
| analysi-approach-data-base | VFDB 2016: hierarchical and refined dataset for big data analysis–10 years on. | 2016 | 184 |
| analysi-approach-data-base | Metabolomics: beyond biomarkers and towards mechanisms. | 2016 | 160 |
| burden-global-diseas-studi | Global, regional, and national life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 1980-2015: a systematic analysis for the Global Burden of Disease Study 2015. | 2016 | 1071 |
| burden-global-diseas-studi | Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015. | 2016 | 534 |
| burden-global-diseas-studi | Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. | 2017 | 484 |
| cancer-gene-express-studi-data | Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA. | 2015 | 48 |
| cancer-gene-express-studi-data | Genetic Mechanisms of Immune Evasion in Colorectal Cancer. | 2018 | 22 |
| cancer-gene-express-studi-data | ISG15 in the tumorigenesis and treatment of cancer: An emerging role in malignancies of the digestive system. | 2016 | 11 |
| cancer-null-report-data | The State of Cancer Care in America, 2016: A Report by the American Society of Clinical Oncology. | 2016 | 43 |
| cancer-null-report-data | AACR Cancer Progress Report 2014. | 2014 | 23 |
| cancer-null-report-data | The evolution of cancer registration. | 2014 | 3 |
| cancer-null-report-data | AACR Cancer Progress Report 2015. | 2015 | 3 |
| cancer-patient-studi-data | The National Cancer Institute’s Dietary Assessment Primer: A Resource for Diet Research. | 2015 | 36 |
| cancer-patient-studi-data | Mechanisms of NAFLD development and therapeutic strategies. | 2018 | 36 |
| cancer-patient-studi-data | Systems analysis of the prostate transcriptome in African-American men compared with European-American men. | 2016 | 21 |
| cancer-patient-studi-data | Precancer Atlas to Drive Precision Prevention Trials. | 2017 | 21 |
| cancer-popul-studi-data | Global, Regional, and National Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life-Years for 29 Cancer Groups, 1990 to 2016: A Systematic Analysis for the Global Burden of Disease Study. | 2018 | 63 |
| cancer-popul-studi-data | Incidence and survival of adult cancer patients in Taiwan, 2002-2012. | 2016 | 56 |
| cancer-popul-studi-data | Reproducibility, reliability and validity of population-based administrative health data for the assessment of cancer non-related comorbidities. | 2017 | 12 |
| cancer-research-patient-data | Gut Microbiota, Inflammation, and Colorectal Cancer. | 2016 | 67 |
| cancer-research-patient-data | Effectiveness of acupuncture and related therapies for palliative care of cancer: overview of systematic reviews. | 2015 | 21 |
| cancer-research-patient-data | Future cancer research priorities in the USA: a Lancet Oncology Commission. | 2017 | 21 |
| cardiovascular-diseas-risk-studi | The Incidence of Major Cardiovascular Events in Immigrants to Ontario, Canada: The CANHEART Immigrant Study. | 2015 | 15 |
| cardiovascular-diseas-risk-studi | Cardiovascular Event Prediction by Machine Learning: The Multi-Ethnic Study of Atherosclerosis. | 2017 | 14 |
| cardiovascular-diseas-risk-studi | The Association of Arsenic Metabolism with Cancer, Cardiovascular Disease, and Diabetes: A Systematic Review of the Epidemiological Evidence. | 2017 | 14 |
| care-health-studi-data | Healthcare Access and Quality Index based on mortality from causes amenable to personal health care in 195 countries and territories, 1990-2015: a novel analysis from the Global Burden of Disease Study 2015. | 2017 | 75 |
| care-health-studi-data | Measuring progress and projecting attainment on the basis of past trends of the health-related Sustainable Development Goals in 188 countries: an analysis from the Global Burden of Disease Study 2016. | 2017 | 53 |
| care-health-studi-data | Mapping under-5 and neonatal mortality in Africa, 2000-15: a baseline analysis for the Sustainable Development Goals. | 2017 | 28 |
| care-patient-health-data | Big data and new knowledge in medicine: the thinking, training, and tools needed for a learning health system. | 2014 | 66 |
| care-patient-health-data | Insights from advanced analytics at the Veterans Health Administration. | 2014 | 52 |
| care-patient-health-data | Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya. | 2016 | 29 |
| clinic-data-learn-studi | Using Big Data to Emulate a Target Trial When a Randomized Trial Is Not Available. | 2016 | 60 |
| clinic-data-learn-studi | Medical big data: promise and challenges. | 2017 | 19 |
| clinic-data-learn-studi | Are Randomized Controlled Trials the (G)old Standard? From Clinical Intelligence to Prescriptive Analytics. | 2016 | 8 |
| confer-intern-challeng-research-health-develop | Making big data useful for health care: a summary of the inaugural mit critical data conference. | 2014 | 18 |
| confer-intern-challeng-research-health-develop | U.S. Physician-Scientist Workforce in the 21st Century: Recommendations to Attract and Sustain the Pipeline. | 2018 | 4 |
| confer-intern-challeng-research-health-develop | Promoting Secondary Analysis of Electronic Medical Records in China: Summary of the PLAGH-MIT Critical Data Conference and Health Datathon. | 2017 | 3 |
| confound-adjust-estim-effect-model-studi-data | Uncertainty in Propensity Score Estimation: Bayesian Methods for Variable Selection and Model Averaged Causal Effects. | 2014 | 12 |
| confound-adjust-estim-effect-model-studi-data | Adjusting for unmeasured confounding in nonrandomized longitudinal studies: a methodological review. | 2017 | 7 |
| confound-adjust-estim-effect-model-studi-data | Bias Analysis for Uncontrolled Confounding in the Health Sciences. | 2017 | 5 |
| data-decis-health-challeng-public-develop | The challenge of big data in public health: an opportunity for visual analytics. | 2014 | 11 |
| data-decis-health-challeng-public-develop | Data mashups: potential contribution to decision support on climate change and health. | 2014 | 7 |
| data-decis-health-challeng-public-develop | If you build it, they will come: unintended future uses of organised health data collections. | 2016 | 7 |
| digit-technologi-health-data | Digital epidemiology. | 2012 | 111 |
| digit-technologi-health-data | Developing and Evaluating Digital Interventions to Promote Behavior Change in Health and Health Care: Recommendations Resulting From an International Workshop. | 2017 | 62 |
| digit-technologi-health-data | Applying and advancing behavior change theories and techniques in the context of a digital health revolution: proposals for more effectively realizing untapped potential. | 2017 | 20 |
| diseas-clinic-research-data | Drug development in Alzheimer’s disease: the path to 2025. | 2016 | 61 |
| diseas-clinic-research-data | Big data analytics to improve cardiovascular care: promise and challenges. | 2016 | 55 |
| diseas-clinic-research-data | Brain-Body Pathways Linking Psychological Stress and Physical Health. | 2015 | 40 |
| effect-result-studi-data | Big Data and Disease Prevention: From Quantified Self to Quantified Communities. | 2013 | 20 |
| effect-result-studi-data | Changing the environment to improve population health: a framework for considering exposure in natural experimental studies. | 2016 | 19 |
| effect-result-studi-data | Weather effects on the patterns of people’s everyday activities: a study using GPS traces of mobile phone users. | 2013 | 9 |
| ehealth-care-health-inform-base-data | How can research keep up with eHealth? Ten strategies for increasing the timeliness and usefulness of eHealth research. | 2014 | 46 |
| ehealth-care-health-inform-base-data | What is eHealth (6)? Development of a Conceptual Model for eHealth: Qualitative Study with Key Informants. | 2017 | 15 |
| ehealth-care-health-inform-base-data | Designing an Electronic Patient Management System for Multiple Sclerosis: Building a Next Generation Multiple Sclerosis Documentation System. | 2016 | 14 |
| epidemiologi-health-data-research | Transforming epidemiology for 21st century medicine and public health. | 2013 | 52 |
| epidemiologi-health-data-research | Using Electronic Health Records for Population Health Research: A Review of Methods and Applications. | 2016 | 41 |
| epidemiologi-health-data-research | Commentary: Epidemiology in the era of big data. | 2015 | 29 |
| epidemiologi-null-health-data | The last two decades of life course epidemiology, and its relevance for research on ageing. | 2016 | 22 |
| epidemiologi-null-health-data | Analysis commons, a team approach to discovery in a big-data environment for genetic epidemiology. | 2017 | 12 |
| epidemiologi-null-health-data | The Future of Cardiovascular Epidemiology. | 2016 | 11 |
| forecast-model-time-data | Accurate estimation of influenza epidemics using Google search data via ARGO. | 2015 | 40 |
| forecast-model-time-data | Global disease monitoring and forecasting with Wikipedia. | 2014 | 39 |
| forecast-model-time-data | Using networks to combine “big data” and traditional surveillance to improve influenza predictions. | 2015 | 17 |
| gene-associ-diseas-studi-data | Pitfalls of predicting complex traits from SNPs. | 2013 | 203 |
| gene-associ-diseas-studi-data | Developing and evaluating polygenic risk prediction models for stratified disease prevention. | 2016 | 77 |
| gene-associ-diseas-studi-data | Analysis of shared heritability in common disorders of the brain. | 2018 | 40 |
| gene-associ-identifi-studi | Rare and low-frequency coding variants alter human adult height. | 2017 | 111 |
| gene-associ-identifi-studi | Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension. | 2016 | 77 |
| gene-associ-identifi-studi | New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk. | 2016 | 63 |
| genom-challeng-research-data | H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa. | 2016 | 27 |
| genom-challeng-research-data | Stakeholder engagement: a key component of integrating genomic information into electronic health records. | 2013 | 25 |
| genom-challeng-research-data | Building a data sharing model for global genomic research. | 2014 | 15 |
| genom-sequenc-base-data | Insights from 20 years of bacterial genome sequencing. | 2015 | 144 |
| genom-sequenc-base-data | IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. | 2017 | 99 |
| genom-sequenc-base-data | Towards structural systems pharmacology to study complex diseases and personalized medicine. | 2014 | 26 |
| healthcar-data-develop-health | Big data analytics in healthcare: promise and potential. | 2014 | 167 |
| healthcar-data-develop-health | Driving Innovation in Health Systems through an Apps-Based Information Economy. | 2015 | 29 |
| healthcar-data-develop-health | Towards Actualizing the Value Potential of Korea Health Insurance Review and Assessment (HIRA) Data as a Resource for Health Research: Strengths, Limitations, Applications, and Strategies for Optimal Use of HIRA Data. | 2017 | 29 |
| hiv-studi-data-health | The changing epidemiology of the global paediatric HIV epidemic: keeping track of perinatally HIV-infected adolescents. | 2013 | 51 |
| hiv-studi-data-health | Methods of using real-time social media technologies for detection and remote monitoring of HIV outcomes. | 2014 | 47 |
| hiv-studi-data-health | Spending on health and HIV/AIDS: domestic health spending and development assistance in 188 countries, 1995-2015. | 2018 | 17 |
| hospit-patient-ag-studi-data | Predicting suicides after psychiatric hospitalization in US Army soldiers: the Army Study To Assess Risk and rEsilience in Servicemembers (Army STARRS). | 2015 | 73 |
| hospit-patient-ag-studi-data | Epidemiology and socioeconomic features of appendicitis in Taiwan: a 12-year population-based study. | 2015 | 12 |
| hospit-patient-ag-studi-data | Automated comparison of last hospital main diagnosis and underlying cause of death ICD10 codes, France, 2008-2009. | 2014 | 7 |
| host-infect-sequenc-genom | 25-Hydroxycholesterol Protects Host against Zika Virus Infection and Its Associated Microcephaly in a Mouse Model. | 2017 | 46 |
| host-infect-sequenc-genom | Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks. | 2017 | 31 |
| host-infect-sequenc-genom | Transferrin receptor 1 is a reticulocyte-specific receptor for Plasmodium vivax. | 2018 | 20 |
| idea-health-research-system-develop | Innovation in academic chemical screening: filling the gaps in chemical biology. | 2013 | 11 |
| idea-health-research-system-develop | OpenFDA: an innovative platform providing access to a wealth of FDA’s publicly available data. | 2016 | 8 |
| idea-health-research-system-develop | Reimagining Human Research Protections for 21st Century Science. | 2016 | 7 |
| imag-clinic-data-studi | A critical review of the first 10 years of candidate gene-by-environment interaction research in psychiatry. | 2011 | 380 |
| imag-clinic-data-studi | Unraveling the miswired connectome: a developmental perspective. | 2014 | 99 |
| imag-clinic-data-studi | Impact of the Alzheimer’s Disease Neuroimaging Initiative, 2004 to 2014. | 2015 | 53 |
| informat-health-system-inform-data | Big Data Application in Biomedical Research and Health Care: A Literature Review. | 2016 | 28 |
| informat-health-system-inform-data | Big Data: Are Biomedical and Health Informatics Training Programs Ready? Contribution of the IMIA Working Group for Health and Medical Informatics Education. | 2014 | 5 |
| informat-health-system-inform-data | Does Informatics Enable or Inhibit the Delivery of Patient-centred, Coordinated, and Quality-assured Care: a Delphi Study. A Contribution of the IMIA Primary Health Care Informatics Working Group. | 2015 | 4 |
| injuri-data-studi-health | Pre-Clinical Traumatic Brain Injury Common Data Elements: Toward a Common Language Across Laboratories. | 2015 | 27 |
| injuri-data-studi-health | Applications for detection of acute kidney injury using electronic medical records and clinical information systems: workgroup statements from the 15(th) ADQI Consensus Conference. | 2016 | 17 |
| injuri-data-studi-health | Utilizing electronic health records to predict acute kidney injury risk and outcomes: workgroup statements from the 15(th) ADQI Consensus Conference. | 2016 | 15 |
| learn-predict-model-data | Big Data and machine learning in radiation oncology: State of the art and future prospects. | 2016 | 33 |
| learn-predict-model-data | Machine Learning and Data Mining Methods in Diabetes Research. | 2017 | 22 |
| learn-predict-model-data | Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records. | 2013 | 18 |
| malaria-transmiss-infect-control-model | Modeling infectious disease dynamics in the complex landscape of global health. | 2015 | 89 |
| malaria-transmiss-infect-control-model | Global Epidemiology of Plasmodium vivax. | 2016 | 71 |
| malaria-transmiss-infect-control-model | Tools and Strategies for Malaria Control and Elimination: What Do We Need to Achieve a Grand Convergence in Malaria? | 2016 | 46 |
| media-social-health-data | Experimental evidence of massive-scale emotional contagion through social networks. | 2014 | 139 |
| media-social-health-data | Behavioral intervention technologies: evidence review and recommendations for future research in mental health. | 2013 | 138 |
| media-social-health-data | A cross-sectional examination of marketing of electronic cigarettes on Twitter. | 2014 | 104 |
| medic-care-research-health-data | Routinely collected data as a strategic resource for research: priorities for methods and workforce. | 2015 | 12 |
| medic-care-research-health-data | Setting a research agenda for interprofessional education and collaborative practice in the context of United States health system reform. | 2016 | 7 |
| medic-care-research-health-data | Biostatistical and medical statistics graduate education. | 2014 | 6 |
| medic-care-research-health-data | Accelerating Research Impact in a Learning Health Care System: VA’s Quality Enhancement Research Initiative in the Choice Act Era. | 2017 | 6 |
| method-applic-data-develop-research | Building better biomarkers: brain models in translational neuroimaging. | 2017 | 72 |
| method-applic-data-develop-research | Twenty-five years of confirmatory adaptive designs: opportunities and pitfalls. | 2016 | 35 |
| method-applic-data-develop-research | Toward Good Read-Across Practice (GRAP) guidance. | 2016 | 23 |
| model-health-research-data-studi | Spatial and temporal epidemiological analysis in the Big Data era. | 2015 | 10 |
| model-health-research-data-studi | Scalable combinatorial tools for health disparities research. | 2014 | 9 |
| model-health-research-data-studi | Using Big Data to Understand the Human Condition: The Kavli HUMAN Project. | 2015 | 9 |
| model-studi-result-data | User Acceptance of Wrist-Worn Activity Trackers Among Community-Dwelling Older Adults: Mixed Method Study. | 2017 | 12 |
| model-studi-result-data | Comparing baseline characteristics between groups: an introduction to the CBCgrps package. | 2017 | 11 |
| model-studi-result-data | Expanding the boundaries of local similarity analysis. | 2013 | 6 |
| null-research-health-data | Big data: The future of biocuration. | 2008 | 206 |
| null-research-health-data | Data Resource Profile: The National Health Information Database of the National Health Insurance Service in South Korea. | 2017 | 55 |
| null-research-health-data | Ethical challenges of big data in public health. | 2015 | 49 |
| null-scienc-health-data | Radiogenomics: radiobiology enters the era of big data and team science. | 2014 | 38 |
| null-scienc-health-data | Patient focused registries can improve health, care, and science. | 2016 | 22 |
| null-scienc-health-data | Enabling a Learning Health System through a Unified Enterprise Data Warehouse: The Experience of the Northwestern University Clinical and Translational Sciences (NUCATS) Institute. | 2015 | 14 |
| null-scienc-health-data | Navigating knowledge landscapes: on health, science, communication, media, and society. | 2015 | 14 |
| null-scienc-health-data | Setting the Agenda for a New Discipline: Population Health Science. | 2016 | 14 |
| nutrit-approach-health-data | Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development. | 2015 | 41 |
| nutrit-approach-health-data | Popular Nutrition-Related Mobile Apps: A Feature Assessment. | 2016 | 19 |
| nutrit-approach-health-data | Precision nutrition for prevention and management of type 2 diabetes. | 2018 | 10 |
| obes-adult-ag-relat-data-studi-health | Variations in the Prevalence of Obesity Among European Countries, and a Consideration of Possible Causes. | 2017 | 10 |
| obes-adult-ag-relat-data-studi-health | The effects of community environmental factors on obesity among Korean adults: a multilevel analysis. | 2014 | 3 |
| obes-adult-ag-relat-data-studi-health | Effect of Maternal Age at Childbirth on Obesity in Postmenopausal Women: A Nationwide Population-Based Study in Korea. | 2016 | 2 |
| obes-adult-ag-relat-data-studi-health | Investigation Of Obesity-Related Mortality Rates In Delaware. | 2017 | 2 |
| obes-adult-ag-relat-data-studi-health | Compliance with Dietary Guidelines Varies by Weight Status: A Cross-Sectional Study of Australian Adults. | 2018 | 2 |
| obes-adult-ag-relat-data-studi-health | Socioeconomic disparities in abdominal obesity over the life course in China. | 2018 | 2 |
| obes-adult-ag-relat-data-studi-health | Estimating the potential impact of the UK government’s sugar reduction programme on child and adult health: modelling study. | 2019 | 2 |
| paper-editori-editor-research | Contributions from the 2016 Literature on Clinical Decision Support. | 2017 | 3 |
| paper-editori-editor-research | Discussion of “Representation of People’s Decisions in Health Information Systems: A Complementary Approach for Understanding Health Care Systems and Population Health”. | 2017 | 1 |
| paper-editori-editor-research | Clinical Information Systems as the Backbone of a Complex Information Logistics Process: Findings from the Clinical Information Systems Perspective for 2016. | 2017 | 1 |
| paper-editori-editor-research | A new community for those involved and interested in diagnosis and prognosis. | 2017 | 1 |
| patient-base-studi-data | Time-varying effects of a text-based smoking cessation intervention for urban adolescents. | 2015 | 9 |
| patient-base-studi-data | Influence of APOE Genotype on Hippocampal Atrophy over Time - An N=1925 Surface-Based ADNI Study. | 2016 | 7 |
| patient-base-studi-data | Applying MetaMap to Medline for identifying novel associations in a large clinical dataset: a feasibility analysis. | 2014 | 6 |
| patient-health-studi-data | Multimorbidity in chronic disease: impact on health care resources and costs. | 2016 | 36 |
| patient-health-studi-data | Characterizing treatment pathways at scale using the OHDSI network. | 2016 | 35 |
| patient-health-studi-data | Successful aging: Advancing the science of physical independence in older adults. | 2015 | 34 |
| pollut-air-studi-health | High-Resolution Air Pollution Mapping with Google Street View Cars: Exploiting Big Data. | 2017 | 22 |
| pollut-air-studi-health | A Survey of Wireless Sensor Network Based Air Pollution Monitoring Systems. | 2015 | 20 |
| pollut-air-studi-health | An association between air pollution and daily outpatient visits for respiratory disease in a heavy industry area. | 2013 | 19 |
| precis-medicin-research-data | Building the foundation for genomics in precision medicine. | 2015 | 78 |
| precis-medicin-research-data | Metabolomics enables precision medicine: “A White Paper, Community Perspective”. | 2016 | 69 |
| precis-medicin-research-data | From big data analysis to personalized medicine for all: challenges and opportunities. | 2015 | 62 |
| precis-null-medicin-health | Medicine. Big data meets public health. | 2014 | 79 |
| precis-null-medicin-health | Precision Public Health for the Era of Precision Medicine. | 2016 | 75 |
| precis-null-medicin-health | Will Precision Medicine Improve Population Health? | 2016 | 40 |
| pregnanc-popul-studi-data | Association Between Methylphenidate and Amphetamine Use in Pregnancy and Risk of Congenital Malformations: A Cohort Study From the International Pregnancy Safety Study Consortium. | 2018 | 7 |
| pregnanc-popul-studi-data | Aortic dissection in pregnancy in England: an incidence study using linked national databases. | 2015 | 5 |
| pregnanc-popul-studi-data | Outcomes Associated With Paroxysmal Supraventricular Tachycardia During Pregnancy. | 2017 | 3 |
| pregnanc-popul-studi-data | Maternal and fetal outcomes of pregnant women with type 1 diabetes, a national population study. | 2017 | 3 |
| public-health-system-commun-inform-data-popul | Big bad data: law, public health, and biomedical databases. | 2013 | 14 |
| public-health-system-commun-inform-data-popul | From urban planning and emergency training to Pokémon Go: applications of virtual reality GIS (VRGIS) and augmented reality GIS (ARGIS) in personal, public and environmental health. | 2017 | 6 |
| public-health-system-commun-inform-data-popul | The EVOTION Decision Support System: Utilizing It for Public Health Policy-Making in Hearing Loss. | 2017 | 1 |
| public-health-system-commun-inform-data-popul | Environmental Public Health Tracking Program Advances and Successes: Highlights From the First 15 Years. | 2017 | 1 |
| public-health-system-commun-inform-data-popul | Public Views on Using Mobile Phone Call Detail Records in Health Research: Qualitative Study. | 2019 | 1 |
| public-health-system-commun-inform-data-popul | Adjusting the focus: A public health ethics approach to data research. | 2019 | 1 |
| research-data-health-identifi | Crowdsourcing–harnessing the masses to advance health and medicine, a systematic review. | 2014 | 75 |
| research-data-health-identifi | Research impact: a narrative review. | 2016 | 21 |
| research-data-health-identifi | Research impact in the community-based health sciences: an analysis of 162 case studies from the 2014 UK Research Excellence Framework. | 2015 | 19 |
| research-data-inform-health | Big data and biomedical informatics: a challenging opportunity. | 2014 | 34 |
| research-data-inform-health | Genetic data and electronic health records: a discussion of ethical, logistical and technological considerations. | 2014 | 24 |
| research-data-inform-health | Has the biobank bubble burst? Withstanding the challenges for sustainable biobanking in the digital era. | 2016 | 19 |
| resist-develop-studi-data | CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. | 2017 | 230 |
| resist-develop-studi-data | Contemporary status of insecticide resistance in the major Aedes vectors of arboviruses infecting humans. | 2017 | 59 |
| resist-develop-studi-data | MEGARes: an antimicrobial resistance database for high throughput sequencing. | 2017 | 36 |
| risk-ag-associ-cardiovascular-studi | Associations of Omega-3 Fatty Acid Supplement Use With Cardiovascular Disease Risks: Meta-analysis of 10 Trials Involving 77<U+202F>917 Individuals. | 2018 | 47 |
| risk-ag-associ-cardiovascular-studi | Measuring Burden of Unhealthy Behaviours Using a Multivariable Predictive Approach: Life Expectancy Lost in Canada Attributable to Smoking, Alcohol, Physical Inactivity, and Diet. | 2016 | 18 |
| risk-ag-associ-cardiovascular-studi | Association of Physical Activity With Risk of Major Cardiovascular Diseases in Chinese Men and Women. | 2017 | 5 |
| risk-diseas-studi-health | Very large database of lipids: rationale and design. | 2013 | 18 |
| risk-diseas-studi-health | Cerebral Amyloid and Hypertension are Independently Associated with White Matter Lesions in Elderly. | 2015 | 16 |
| risk-diseas-studi-health | Education and coronary heart disease: mendelian randomisation study. | 2017 | 16 |
| risk-patient-cohort-studi | Proton Pump Inhibitors and Risk of Incident CKD and Progression to ESRD. | 2016 | 54 |
| risk-patient-cohort-studi | Impact of diabetes on hospital admission and length of stay among a general population aged 45 year or more: a record linkage study. | 2015 | 13 |
| risk-patient-cohort-studi | Intradialytic hypotension, blood pressure changes and mortality risk in incident hemodialysis patients. | 2018 | 7 |
| scienc-research-data-health | What is a representative brain? Neuroscience meets population science. | 2013 | 35 |
| scienc-research-data-health | Nature Contact and Human Health: A Research Agenda. | 2017 | 31 |
| scienc-research-data-health | Advancing Symptom Science Through Use of Common Data Elements. | 2015 | 17 |
| sensor-health-develop-data-base | A framework for using GPS data in physical activity and sedentary behavior studies. | 2015 | 44 |
| sensor-health-develop-data-base | Data mining for wearable sensors in health monitoring systems: a review of recent trends and challenges. | 2013 | 42 |
| sensor-health-develop-data-base | Devices for Self-Monitoring Sedentary Time or Physical Activity: A Scoping Review. | 2016 | 32 |
| surveil-public-health-data | Approaches to canine health surveillance. | 2014 | 33 |
| surveil-public-health-data | Infectious Disease Surveillance in the Big Data Era: Towards Faster and Locally Relevant Systems. | 2016 | 18 |
| surveil-public-health-data | Big Data for Infectious Disease Surveillance and Modeling. | 2016 | 17 |
| toxicologi-approach-data-develop-health | FutureTox II: in vitro data and in silico models for predictive toxicology. | 2015 | 18 |
| toxicologi-approach-data-develop-health | Neonatal abstinence syndrome: Pharmacologic strategies for the mother and infant. | 2016 | 12 |
| toxicologi-approach-data-develop-health | Systems Toxicology: Real World Applications and Opportunities. | 2017 | 12 |
| transmiss-infect-model-diseas-control-data | Virus genomes reveal factors that spread and sustained the Ebola epidemic. | 2017 | 66 |
| transmiss-infect-model-diseas-control-data | Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study. | 2016 | 25 |
| transmiss-infect-model-diseas-control-data | Updates to the zoonotic niche map of Ebola virus disease in Africa. | 2016 | 14 |
| vaccin-develop-data-health | Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study. | 2017 | 41 |
| vaccin-develop-data-health | Systems vaccinology: Enabling rational vaccine design with systems biological approaches. | 2015 | 37 |
| vaccin-develop-data-health | The Humoral Immune Response to HCV: Understanding is Key to Vaccine Development. | 2014 | 24 |
Use of keywords
We can review the commonest Mesh headings associated with each cluster tag.
labels$results %>%
left_join(search1, by = c("pmid.value" = "pmid")) %>%
select(clus_names, mesh) %>%
filter(mesh != "NULL") %>%
unnest(mesh) %>%
count(clus_names, mesh,sort = TRUE) %>%
filter(n < 30) %>%
ungroup() %>%
group_by(clus_names) %>%
top_n(10) %>%
mutate(summary = paste(mesh, collapse = "; " )) %>%
select(-c(mesh, n)) %>%
distinct() %>%
arrange(clus_names) %>%
knitr::kable()| clus_names | summary |
|---|---|
| abstract-meet-annual-null | Humans; Animals; Delivery of Health Care; United States; Accreditation; Africa; Annual Reports as Topic; Biomedical Research; Canada; Career Choice; Career Mobility; Chicago; Clinical Competence; Committee Membership; Disease Outbreaks; Education, Medical, Graduate; Education, Pharmacy; Forecasting; Global Health; Healthy People Programs; History, 20th Century; Influenza Pandemic, 1918-1919; Influenza, Human; Information Management; Information Services; Internal Medicine; Internship and Residency; Job Description; Libraries, Digital; Libraries, Medical; Library Associations; Library Services; Marijuana Smoking; Medical Marijuana; Mental Disorders; Neuropharmacology; Ohio; Organizational Objectives; Organizational Policy; Pandemics; Patient Advocacy; Physicians; Primary Health Care; Psychopharmacology; Psychotropic Drugs; Quality Indicators, Health Care; Societies; Societies, Medical; Societies, Pharmaceutical; Socioeconomic Factors; Surgeons; Women’s Health |
| ag-associ-risk-studi | Humans; Male; Adult; Aged; Female; Middle Aged; Prospective Studies; Risk Factors; Aged, 80 and over; Smoking |
| ag-nation-health-studi | Humans; Female; Male; Republic of Korea; Adult; Middle Aged; Aged; Databases, Factual; Health Surveys; Prevalence; Risk Factors |
| ag-popul-studi-result | Humans; Female; Male; Adolescent; Infant, Newborn; Adult; Age Factors; Aged; Aged, 80 and over; Case-Control Studies; Child; Child, Preschool; Infant; Time Factors; Young Adult |
| ai-artifici-intellig-health | Artificial Intelligence; Big Data; Humans; Communicable Disease Control; Communicable Diseases; Communication; Disaster Planning; Disasters; Disease Eradication; Israel; Malaria; Public Health; Risk Management |
| analysi-approach-data-base | Humans; Genomics; Computational Biology; Algorithms; Databases, Factual; Animals; Software; Female; Data Mining; Male; Models, Statistical |
| burden-global-diseas-studi | Female; Global Burden of Disease; Male; Adult; Middle Aged; Aged; Child; Adolescent; Child, Preschool; Infant |
| cancer-gene-express-studi-data | Humans; Female; Databases, Genetic; Genomics; Aged; Breast Neoplasms; DNA Copy Number Variations; Gene Expression Regulation, Neoplastic; Male; Neoplasms; Polymorphism, Single Nucleotide; Prognosis |
| cancer-null-report-data | Humans; Neoplasms; Medical Oncology; Animals; Accidental Falls; Artificial Intelligence; Automation; Biomedical Research; Breast Neoplasms; Computational Biology; Confidentiality; Data Mining; Decision Making, Computer-Assisted; Delivery of Health Care; Diabetes Mellitus, Type 1; Diagnosis, Computer-Assisted; Economics, Behavioral; Female; Government Programs; Health Behavior; Health Care Costs; Health Services Accessibility; History, 21st Century; Image Interpretation, Computer-Assisted; Insurance, Health; Interinstitutional Relations; Magnetic Resonance Imaging; Metabolomics; Models, Organizational; Molecular Diagnostic Techniques; Motivation; Organizational Objectives; Population Surveillance; Proteomics; Quality of Health Care; Registries; Research Report; Tomography, X-Ray Computed; United States |
| cancer-patient-studi-data | Male; Adult; Aged, 80 and over; Neoplasms; Breast Neoplasms; Risk Factors; Cohort Studies; Colorectal Neoplasms; Algorithms; Databases, Factual; Kaplan-Meier Estimate; Prognosis; Retrospective Studies; United States |
| cancer-popul-studi-data | Humans; Female; Middle Aged; Male; Adult; Aged; Neoplasms; Incidence; Cohort Studies; Risk Factors |
| cancer-research-patient-data | Humans; Neoplasms; Treatment Outcome; United States; Databases, Factual; Delivery of Health Care; Forecasting; Information Systems; Medical Oncology; Palliative Care |
| cardiovascular-diseas-risk-studi | Humans; Cardiovascular Diseases; Female; Male; Risk Factors; Aged; Middle Aged; Biomarkers; Cohort Studies; Risk Assessment |
| care-health-studi-data | Humans; Female; Male; Aged; Hospitalization; Middle Aged; Age Factors; Delivery of Health Care; Global Burden of Disease; Sex Factors |
| care-patient-health-data | Humans; Electronic Health Records; Data Mining; Datasets as Topic; Delivery of Health Care; Medical Informatics; United States; Software; Biomedical Research; Data Collection; Databases, Factual; Quality Improvement; Quality of Health Care; Registries |
| clinic-data-learn-studi | Humans; Electronic Health Records; Databases, Factual; Randomized Controlled Trials as Topic; Algorithms; Big Data; Data Mining; Observational Studies as Topic; Accidents, Occupational; Adult; Ambulatory Care Facilities; Biomedical Research; Breast Neoplasms; Causality; China; Clinical Studies as Topic; Clinical Trials as Topic; Comparative Effectiveness Research; Computer-Assisted Instruction; Computer Simulation; Construction Industry; Critical Illness; Data Analysis; Data Interpretation, Statistical; Database Management Systems; Decision Making; Drug Therapy, Combination; Estrogen Replacement Therapy; Female; Forecasting; Informed Consent; Intelligence; Intensive Care Units; Medical Informatics Applications; Models, Theoretical; Occupational Health; Ophthalmology; Pharmaceutical Preparations; Population Health Management; Postmenopause; Progestins; Propensity Score; Rare Diseases; Research Design; Research Subjects; Respiration, Artificial; Safety Management; Software; Tidal Volume; Treatment Outcome; User-Computer Interface; Ventilators, Mechanical; Virtual Reality; Workflow |
| confer-intern-challeng-research-health-develop | Humans; Advisory Committees; Anniversaries and Special Events; Biomedical Research; Canada; China; Congresses as Topic; Consensus; Consensus Development Conferences as Topic; Data Mining; Databases as Topic; Europe; Food; Food Quality; Harm Reduction; Health Status Disparities; History, 20th Century; History, 21st Century; Information Dissemination; Internet; Medical Informatics; Mycotoxins; Physicians; Public Health; Public Health Administration; Public Health Informatics; Public Health Systems Research; Registries; Research Personnel; Retrospective Studies; Social Justice; Social Media; Societies; Socioeconomic Factors; Technology; United States; Violence; Washington; Workforce |
| confound-adjust-estim-effect-model-studi-data | Humans; Bias; Confounding Factors (Epidemiology); Propensity Score; Research Design; Algorithms; Computer Simulation; Female; Logistic Models; Male; Multivariate Analysis |
| data-decis-health-challeng-public-develop | Humans; Data Collection; Data Mining; Decision Support Techniques; Algorithms; Animals; Climate Change; Databases, Factual; Decision Making; Dual Use Research; Evidence-Based Practice; Health; Health Planning; Healthy Lifestyle; Human Rights; Information Dissemination; Informed Consent; Internet; Knowledge; Mental Health; Mental Health Services; Neural Networks (Computer); Policy; Privacy; Public Health; Records; Regional Health Planning; Safety; Spain; Systems Analysis; Technology; Veterinary Medicine |
| digit-technologi-health-data | Humans; Telemedicine; Computer Security; Internet; Delivery of Health Care; Developing Countries; Electronic Health Records; Health Behavior; Public Health; Social Media; Software |
| diseas-clinic-research-data | Humans; Cardiovascular Diseases; Databases, Factual; Biomedical Research; United States; Animals; Data Mining; Diffusion of Innovation; Electronic Health Records; Exercise; Forecasting; Information Dissemination; National Heart, Lung, and Blood Institute (U.S.) |
| effect-result-studi-data | Humans; Cities; Air Pollutants; China; Environmental Monitoring; Air Pollution; Environmental Exposure; Particulate Matter; Spatial Analysis; Urbanization |
| ehealth-care-health-inform-base-data | Humans; Telemedicine; Delivery of Health Care; Internet; Randomized Controlled Trials as Topic; Research Design; Adult; Behavior Therapy; Biomedical Research; Cell Phone; Communication; Data Mining; Decision Making; Evidence-Based Medicine; Female; Health Literacy; Health Promotion; History, 20th Century; Male; Medical Informatics; Mental Health; Middle Aged; Neoplasms; Obesity; Pathology, Clinical; Patient Participation; Physician-Patient Relations; Precision Medicine; Primary Health Care; Qualitative Research; Quality Improvement; Research; Self Care; Social Support; Weight Loss |
| epidemiologi-health-data-research | Humans; Public Health; Epidemiology; Epidemiologic Methods; Epidemiologic Studies; Research Design; Data Collection; United States; Artificial Intelligence; Biomedical Research; Forecasting; Health Behavior; History, 21st Century; Precision Medicine |
| epidemiologi-null-health-data | Humans; Epidemiologic Methods; Big Data; Biomedical Research; Confidentiality; Data Mining; Epidemiology; Forecasting; Public Health; Research |
| forecast-model-time-data | Humans; Influenza, Human; Forecasting; Internet; Models, Statistical; Incidence; China; Epidemics; Models, Theoretical; Public Health; Time Factors; United States |
| gene-associ-diseas-studi-data | Humans; Genome-Wide Association Study; Phenotype; Genetic Variation; Genomics; Genotype; Male; Models, Genetic; Polymorphism, Single Nucleotide; Algorithms; Animals; Gene-Environment Interaction; Genetic Predisposition to Disease; Transcriptome |
| gene-associ-identifi-studi | Female; Genetic Predisposition to Disease; Male; Polymorphism, Single Nucleotide; Phenotype; Adult; Case-Control Studies; Middle Aged; Quantitative Trait Loci; Aged; Body Mass Index; European Continental Ancestry Group; Genetic Loci; Genetic Variation |
| genom-challeng-research-data | Humans; Genomics; Genome, Human; Computational Biology; High-Throughput Nucleotide Sequencing; Information Dissemination; Electronic Health Records; Genetics, Medical; Infant, Newborn; Neonatal Screening; Precision Medicine; Translational Medical Research; United States |
| genom-sequenc-base-data | Genomics; Sequence Analysis, DNA; Genome, Bacterial; Humans; Bacteria; Computational Biology; Phylogeny; Software; Animals; Genetic Variation; High-Throughput Nucleotide Sequencing; Internet; Reproducibility of Results; Species Specificity; Transcriptome |
| healthcar-data-develop-health | Humans; Delivery of Health Care; Data Mining; Databases, Factual; Decision Making; Adult; Aged; Confidentiality; Datasets as Topic; Female; Information Dissemination; Information Storage and Retrieval; Internet; Male; Middle Aged; Organizational Innovation; Outcome Assessment (Health Care); Precision Medicine; Reproducibility of Results; Telemedicine |
| hiv-studi-data-health | Male; Female; Adult; Public Health; Adolescent; HIV-1; Middle Aged; Social Media; Viral Load; Young Adult |
| hospit-patient-ag-studi-data | Humans; Female; Middle Aged; Male; Aged; Adult; Young Adult; Aged, 80 and over; Adolescent; Retrospective Studies; Taiwan |
| host-infect-sequenc-genom | Humans; Animals; Host-Parasite Interactions; Malaria; Phylogeny; Transcriptome; Algorithms; Computational Biology; Disease Models, Animal; Disease Transmission, Infectious; Ebolavirus; Genome, Viral; Genotype; Membrane Proteins; MicroRNAs; Mutation; Mycobacterium tuberculosis; Oligonucleotides; Orthomyxoviridae; Plasmodium; Plasmodium vivax; Protozoan Proteins; RNA, Messenger; Software |
| idea-health-research-system-develop | Humans; Animals; Data Mining; Forecasting; History, 21st Century; Internet; Research; Software; Adverse Drug Reaction Reporting Systems; Algorithms; Bayes Theorem; Biology; Biomedical Research; Chemistry; Computer Graphics; Consent Forms; Cooperative Behavior; Critical Care; Curriculum; Databases, Factual; Datasets as Topic; Decision Making; Decision Support Systems, Clinical; Delivery of Health Care; Drug Development; Drug Evaluation, Preclinical; Drug Industry; Drug Labeling; Education, Graduate; Electronic Health Records; Europe; Female; Government Regulation; Health Behavior; Health Knowledge, Attitudes, Practice; Health Promotion; High-Throughput Screening Assays; History, 16th Century; History, 17th Century; History, 18th Century; History, 19th Century; History, 20th Century; History, Ancient; Human Experimentation; Industry; Information Dissemination; Informed Consent; Inventions; Life Style; Logic; Male; Medical Informatics; Medical Informatics Applications; Mobile Applications; Models, Statistical; One Health; Ownership; Phenotype; Private Sector; Probability; Product Recalls and Withdrawals; Programming Languages; Public Health; Public Sector; Research Design; Science; Social Responsibility; Statistics as Topic; Telemedicine; United States; United States Food and Drug Administration |
| imag-clinic-data-studi | Female; Male; Image Processing, Computer-Assisted; Algorithms; Biomarkers; Diagnostic Imaging; Adult; Aged; Alzheimer Disease; Magnetic Resonance Imaging |
| informat-health-system-inform-data | Medical Informatics; Humans; Societies, Medical; Patient Participation; Public Health Informatics; Telemedicine; Bibliometrics; Biological Ontologies; Communication; Computer Security; Confidentiality; Consensus; Consumer Health Informatics; Consumer Health Information; Data Anonymization; Datasets as Topic; Delphi Technique; Epidemiology; Forecasting; Genomics; Global Health; Health Equity; History, 20th Century; History, 21st Century; Informatics; Information Systems; Meaningful Use; Patient-Centered Care; Periodicals as Topic; Population Health; Precision Medicine; Privacy; Quality Assurance, Health Care; Social Media; Software; United States |
| injuri-data-studi-health | Humans; Female; Male; Child; Child, Preschool; New South Wales; Oceanic Ancestry Group; Adolescent; Infant; Hospitalization; Infant, Newborn |
| learn-predict-model-data | Humans; Machine Learning; Algorithms; Female; Male; Databases, Factual; Electronic Health Records; Data Mining; Middle Aged; ROC Curve; Support Vector Machine |
| malaria-transmiss-infect-control-model | Animals; Malaria; Malaria, Falciparum; Child, Preschool; Global Health; Infant; Prevalence; Communicable Disease Control; Female; Insect Vectors; Male |
| media-social-health-data | Internet; Female; Male; Adolescent; Adult; Social Networking; Information Dissemination; Public Health; Public Opinion; Social Support; Young Adult |
| medic-care-research-health-data | Humans; Cooperative Behavior; United States; Public Health; Interprofessional Relations; Patient-Centered Care; Quality of Health Care; Research; Biomedical Research; Child; Child Welfare; Cost-Benefit Analysis; Data Collection; Delivery of Health Care; Evidence-Based Medicine; Health Personnel; History, 20th Century; History, 21st Century; Holistic Health |
| method-applic-data-develop-research | Humans; Databases, Factual; Information Storage and Retrieval; Software; Algorithms; Animals; Artificial Intelligence; Bibliometrics; Biomarkers; Biometry; Brain; Brain Mapping; Chemical Safety; Clinical Trials as Topic; Cloud Computing; Computer Simulation; Data Interpretation, Statistical; Data Mining; Database Management Systems; Datasets as Topic; Endpoint Determination; Hazardous Substances; History, 20th Century; History, 21st Century; Image Processing, Computer-Assisted; Medical Informatics; Meta-Analysis as Topic; Metabolomics; Models, Theoretical; Neuroimaging; Pattern Recognition, Physiological; Reproducibility of Results; Research Design; Risk Assessment; Safety Management; Sample Size; Software Design; Toxicology; Uncertainty; User-Computer Interface; Workflow |
| model-health-research-data-studi | Humans; Algorithms; Models, Theoretical; China; Delivery of Health Care; Geographic Information Systems; Health Services Accessibility; Research; Adult; Animal Diseases; Animals; Attitude; Catchment Area (Health); Cities; Cloud Computing; Commerce; Consumer Behavior; Costs and Cost Analysis; Crowdsourcing; Data Analysis; Data Collection; Data Interpretation, Statistical; Databases as Topic; Databases, Factual; Decision Making; Entropy; Environmental Exposure; Environmental Health; Environmental Monitoring; Epidemiologic Research Design; Food Safety; Fuzzy Logic; Garbage; Gene-Environment Interaction; Gravitation; Health; Health Impact Assessment; Health Personnel; Health Plan Implementation; Health Resources; Health Status Disparities; Industry; Information Services; Internet; Longitudinal Studies; Medically Underserved Area; Motor Activity; Motor Vehicles; Physicians; Probability; Program Evaluation; Public Health; Railroads; Recycling; Refuse Disposal; Remote Sensing Technology; Reproducibility of Results; Research Design; Risk Management; Rural Population; Safety Management; Socioeconomic Factors; Spatio-Temporal Analysis; Technology; Time Factors; Travel; Uncertainty; United States |
| model-studi-result-data | Humans; Female; Adult; Algorithms; Data Mining; Electronic Health Records; Male; Middle Aged; Models, Theoretical; Young Adult |
| null-research-health-data | Public Health; Biomedical Research; United States; Data Mining; Data Collection; Female; Male; Electronic Health Records; Datasets as Topic; Statistics as Topic |
| null-scienc-health-data | Humans; Science; Health Services Research; Information Dissemination; Translational Medical Research; Computational Biology; Data Interpretation, Statistical; Genomics; Models, Statistical; United States |
| nutrit-approach-health-data | Humans; Health Promotion; Nutrition Policy; Diet; Female; United States; Child; Databases, Factual; Feeding Behavior; Gastrointestinal Microbiome; Healthy Diet; Nutritional Status; Precision Medicine |
| obes-adult-ag-relat-data-studi-health | Humans; Body Mass Index; Female; Male; Middle Aged; Obesity; Prevalence; Adult; Aged; Diet; Ethnic Groups; Health Surveys; Pediatric Obesity; Risk Factors |
| paper-editori-editor-research | Humans; Electronic Health Records; Information Dissemination; Medical Informatics; Clinical Decision-Making; Data Mining; Decision Support Systems, Clinical; Biomedical Research; Comparative Effectiveness Research; Confidentiality; Data Anonymization; Datasets as Topic; Decision Making; Decision Support Techniques; Drug Interactions; Health Information Systems; Information Storage and Retrieval; Information Systems; Informed Consent; Internationality; Medical Order Entry Systems; Models, Organizational; Natural Language Processing; Patient Acceptance of Health Care; Patient Care Team; Peer Review; Quality Control; Societies, Medical |
| patient-base-studi-data | Humans; Male; Female; Aged; Middle Aged; Adult; Adolescent; Aged, 80 and over; Alzheimer Disease; Calibration; Logistic Models; Risk Factors; Time Factors; Treatment Outcome |
| patient-health-studi-data | Female; Male; Middle Aged; Aged; Adult; Electronic Health Records; Databases, Factual; Young Adult; Aged, 80 and over; Adolescent |
| pollut-air-studi-health | Air Pollution; Humans; Air Pollutants; Female; Particulate Matter; Male; China; Environmental Monitoring; Environmental Exposure; Aged; Middle Aged |
| precis-medicin-research-data | Genomics; Evidence-Based Medicine; Databases, Factual; Biomedical Research; Systems Biology; Translational Medical Research; Delivery of Health Care; Electronic Health Records; Animals; Biomarkers |
| precis-null-medicin-health | Humans; Precision Medicine; Public Health; Biomedical Research; Computational Biology; Diagnostic Imaging; Education, Medical; Genomics; History, 21st Century; Medical Informatics; United States |
| pregnanc-popul-studi-data | Adult; Female; Humans; Pregnancy; Cohort Studies; Adolescent; Pregnancy Outcome; Cesarean Section; Databases, Factual; Infant, Newborn; Pregnancy Complications; Pregnancy Trimester, First; Premature Birth; Prevalence; Smoking; Young Adult |
| public-health-system-commun-inform-data-popul | Humans; Public Health; Health Policy; Causality; Chicago; City Planning; Civil Defense; Data Interpretation, Statistical; Decision Making; Decision Support Techniques; Electronic Health Records; Environmental Health; Epidemiologic Factors; Epidemiologic Studies; Geographic Information Systems; Government Regulation; Hearing Loss; Information Storage and Retrieval; Mobile Applications; Nutrition Policy; Policy Making; Population Surveillance; Public Health Practice; Public Policy; Public Sector; Quality Control; United States; User-Computer Interface; Video Games |
| research-data-health-identifi | Humans; Research Design; Public Health; Biomedical Research; United Kingdom; Adolescent; Australia; Child; Cost-Benefit Analysis; Decision Making; Dental Research; Female; Male; Regression Analysis; Translational Medical Research |
| research-data-inform-health | Humans; Biomedical Research; Information Dissemination; Informed Consent; Confidentiality; Female; Male; Medical Informatics; Reproducibility of Results; Adult; Data Mining; Databases, Factual; Internet; Models, Theoretical; United States |
| research-health-data-studi | Information Storage and Retrieval; Models, Statistical; Social Media; Prevalence; Research Design; Information Dissemination; Infant; Population Surveillance; Cardiovascular Diseases; Child, Preschool; Models, Theoretical |
| resist-develop-studi-data | Humans; Animals; Anti-Bacterial Agents; Drug Resistance, Microbial; Insecticide Resistance; Arboviruses; Mosquito Control; Mosquito Vectors; Aedes; Arbovirus Infections; Insecticides; Metagenomics; Streptococcus pneumoniae |
| risk-ag-associ-cardiovascular-studi | Humans; Female; Male; Aged; Middle Aged; Adult; Child; Cohort Studies; Adolescent; Aged, 80 and over; Cardiovascular Diseases; Hypertension; Incidence; Myocardial Infarction; Obesity; Risk Factors; Sex Factors; Smoking; Stroke; Taiwan |
| risk-diseas-studi-health | Humans; Female; Male; Middle Aged; Adult; Risk Factors; Aged; Hypertension; Prevalence; Taiwan |
| risk-patient-cohort-studi | Female; Humans; Male; Middle Aged; Aged; Adult; Diabetes Mellitus, Type 2; Risk Factors; Adolescent; Aged, 80 and over; China; Comorbidity; Hospitalization; Kidney Failure, Chronic; Young Adult |
| scienc-research-data-health | Humans; Biomedical Research; United States; Translational Medical Research; Science; Animals; Computational Biology; Cooperative Behavior; National Institutes of Health (U.S.); Public Health; Research Design |
| sensor-health-develop-data-base | Humans; Exercise; Mobile Applications; Telemedicine; Geographic Information Systems; Internet; Monitoring, Physiologic; Public Health; Time Factors; Adolescent; Adult; Algorithms; Benchmarking; Biomedical Research; Biosensing Techniques; Environmental Monitoring; Female; Male; Monitoring, Ambulatory; Sedentary Lifestyle; Surveys and Questionnaires; Wearable Electronic Devices |
| surveil-public-health-data | Humans; Communicable Diseases; Population Surveillance; Disease Outbreaks; Epidemiological Monitoring; Internet; Public Health Surveillance; Databases, Factual; Influenza, Human; Adolescent; Child; Child, Preschool; China; Communicable Diseases, Emerging; Data Collection; Electronic Data Processing; Information Dissemination; Insurance Claim Review; Models, Statistical; Public Health; Retrospective Studies; United States |
| toxicologi-approach-data-develop-health | Humans; Analgesics, Opioid; Toxicology; Animals; Computer Simulation; Female; Practice Patterns, Physicians’; United States; Aged; Animal Testing Alternatives; Australia; Drug Prescriptions; In Vitro Techniques; Male; Middle Aged; Opioid-Related Disorders; Toxicity Tests |
| transmiss-infect-model-diseas-control-data | Humans; Animals; Disease Outbreaks; Hemorrhagic Fever, Ebola; Communicable Diseases; Databases, Factual; Epidemiological Monitoring; Models, Theoretical; Data Collection; Female |
| vaccin-develop-data-health | Vaccination; Vaccines; Influenza Vaccines; Influenza, Human; United States; Female; Aged; Health Knowledge, Attitudes, Practice; Immunization Programs; Infant; Male; Social Media; Socioeconomic Factors; Systems Biology; Vaccination Coverage |
Investigating individial themes to identify full-text articles
Lets explore articles for which public health is a Mesh heading.
ph <- labels$results %>%
left_join(search1, by = c("pmid.value" = "pmid")) %>%
filter(str_detect(keywords, "Public Health"))
ph %>%
count(clus_names, sort = TRUE)
#> # A tibble: 39 x 2
#> clus_names n
#> <chr> <int>
#> 1 research-health-data-studi 76
#> 2 null-research-health-data 21
#> 3 epidemiologi-health-data-research 13
#> 4 media-social-health-data 10
#> 5 hiv-studi-data-health 8
#> 6 precis-medicin-research-data 5
#> 7 surveil-public-health-data 5
#> 8 cancer-patient-studi-data 4
#> 9 digit-technologi-health-data 4
#> 10 forecast-model-time-data 4
#> # ... with 29 more rowsThere is one article tagged with ai-intellig-artifici-health-data which has Public Health as a mesh heading. We can use epmc_ftxt to extract the full text article.
library(rvest)
get_pmcids <- ph %>%
filter(clus_names == "data-research-health-develop") %>%
select(id, pmcid) %>%
filter(!is.na(pmcid))
details <- mutate(ids, details = map(get_ids, epmc_details))
full_text <- details %>%
mutate(full_text = map(details, "ftx")) %>%
unnest(full_text) %>%
filter(availability == "Free") %>%
left_join(get_pmcids, by = c("value" = "id")) %>%
distinct()
full_text <- europepmc::epmc_ftxt("PMC5171550")
ft <- full_text %>%
html_text()
ft %>%
str_split(., "\\. ") %>%
enframe() %>%
formattable::formattable()
Finally we can gather all the abstracts into a single interactive table which can be searched, filtered and shared.
labels$results %>%
left_join(search1, by = c("pmid.value" = "pmid")) %>%
select(cluster, clus_names, doi, title, journalTitle, pubYear, citedByCount, absText) %>%
mutate(doi = paste0("<a href = https://", doi, ">doi</a>")) %>%
DT::datatable(escape = FALSE, extensions = c('Responsive','Buttons', 'FixedHeader'),
filter = "top",
options = list(
autoWidth = TRUE,
columnDefs = list(list(width = '450px')),
dom = 'Bfrtip',
buttons = c('csv', 'excel'),
fixedHeader=TRUE)
)